Inferring paternal history of rural African‐derived Brazilian populations from Y chromosomes

Kimura, Lilian; Nunes, Kelly; Macedo‐Souza, Lúcia Inês; Rocha, Jorge; Meyer, Diogo; Mingroni-Netto, Regina Célia

doi:10.1002/ajhb.22930

Cited by 6 publications

(7 citation statements)

References 26 publications

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“…The present-day pool of Native American Y chromosomes is a mixture of haplogroups that derive from pre-Columbian dispersals from Siberia and more recent gene flow from Europe and Africa (Grugni et al 2015; Kimura et al 2016; Roewer et al 2013; Zegura et al 2004). The diversity derived from the first dispersals is restricted to just two founding lineages within haplogroup Q and one or two in haplogroup C3-M217 (Fig.…”

Section: Ancient Y Chromosomes Of the Native Americansmentioning

confidence: 99%

The study of human Y chromosome variation through ancient DNA

Kivisild

2017

Hum Genet

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High throughput sequencing methods have completely transformed the study of human Y chromosome variation by offering a genome-scale view on genetic variation retrieved from ancient human remains in context of a growing number of high coverage whole Y chromosome sequence data from living populations from across the world. The ancient Y chromosome sequences are providing us the first exciting glimpses into the past variation of male-specific compartment of the genome and the opportunity to evaluate models based on previously made inferences from patterns of genetic variation in living populations. Analyses of the ancient Y chromosome sequences are challenging not only because of issues generally related to ancient DNA work, such as DNA damage-induced mutations and low content of endogenous DNA in most human remains, but also because of specific properties of the Y chromosome, such as its highly repetitive nature and high homology with the X chromosome. Shotgun sequencing of uniquely mapping regions of the Y chromosomes to sufficiently high coverage is still challenging and costly in poorly preserved samples. To increase the coverage of specific target SNPs capture-based methods have been developed and used in recent years to generate Y chromosome sequence data from hundreds of prehistoric skeletal remains. Besides the prospects of testing directly as how much genetic change in a given time period has accompanied changes in material culture the sequencing of ancient Y chromosomes allows us also to better understand the rate at which mutations accumulate and get fixed over time. This review considers genome-scale evidence on ancient Y chromosome diversity that has recently started to accumulate in geographic areas favourable to DNA preservation. More specifically the review focuses on examples of regional continuity and change of the Y chromosome haplogroups in North Eurasia and in the New World.

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Section: Ancient Y Chromosomes Of the Native Americansmentioning

confidence: 99%

The study of human Y chromosome variation through ancient DNA

Kivisild

2017

Hum Genet

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“…The present study was performed in an admixed Brazilian isolate located in the Ribeira River Valley, in the southern part of the State of São Paulo, Brazil ( Fig 1 ). This isolate, known in Brazil as a quilombo , was founded around 1890 by runaway, abandoned and freed slaves (some of them being the admixed offspring of white farm owners and African female slaves) and a few pure or mixed native Americans, who created small rural settlements in isolated areas inside the Atlantic rainforest for several generations (other details of interest on the quilombo population structure and demography are described elsewhere [ 1 , 19 , 21 ]). The isolate aggregates twelve communities that were treated as a single one, since the degree of differentiation among its communities is very low, with F ST indices generally smaller than 0.05 [ 1 ].…”

Section: Methodsmentioning

confidence: 99%

Inbreeding estimates in human populations: Applying new approaches to an admixed Brazilian isolate

et al. 2018

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The analysis of genomic data (~400,000 autosomal SNPs) enabled the reliable estimation of inbreeding levels in a sample of 541 individuals sampled from a highly admixed Brazilian population isolate (an African-derived quilombo in the State of São Paulo). To achieve this, different methods were applied to the joint information of two sets of markers (one complete and another excluding loci in patent linkage disequilibrium). This strategy allowed the detection and exclusion of markers that biased the estimation of the average population inbreeding coefficient (Wright’s fixation index FIS), which value was eventually estimated as around 1% using any of the methods we applied. Quilombo demographic inferences were made by analyzing the structure of runs of homozygosity (ROH), which were adapted to cope with a highly admixed population with a complex foundation history. Our results suggest that the amount of ROH <2Mb of admixed populations should be somehow proportional to the genetic contribution from each parental population.

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“…Currently, there are more than 5,970 remaining quilombos (areas protected by the government where these populations live; IBGE, 2010 19 ), between the North and South regions, with a community concentration formed by 100–400 individuals in Southeast Brazil ( Santos and Tatto, 2008 ). However, no more than 30 communities have been analyzed regarding their genomic background ( Kimura et al, 2017 ). In general, Quilombola communities are deprived of treated water sources, garbage collection, and sewage ( Galindo et al, 2012 ), which could expose the residents to harmful substances and mutagenic agents.…”

Section: The Communities Of Enslaved Sub-saharan African Descendants:...mentioning

confidence: 99%

A review of ancestrality and admixture in Latin America and the caribbean focusing on native American and African descendant populations

Oliveira

Secolin²,

Lopes-Cendes³

2023

Front. Genet.

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Genomics can reveal essential features about the demographic evolution of a population that may not be apparent from historical elements. In recent years, there has been a significant increase in the number of studies applying genomic epidemiological approaches to understand the genetic structure and diversity of human populations in the context of demographic history and for implementing precision medicine. These efforts have traditionally been applied predominantly to populations of European origin. More recently, initiatives in the United States and Africa are including more diverse populations, establishing new horizons for research in human populations with African and/or Native ancestries. Still, even in the most recent projects, the under-representation of genomic data from Latin America and the Caribbean (LAC) is remarkable. In addition, because the region presents the most recent global miscegenation, genomics data from LAC may add relevant information to understand population admixture better. Admixture in LAC started during the colonial period, in the 15th century, with intense miscegenation between European settlers, mainly from Portugal and Spain, with local indigenous and sub-Saharan Africans brought through the slave trade. Since, there are descendants of formerly enslaved and Native American populations in the LAC territory; they are considered vulnerable populations because of their history and current living conditions. In this context, studying LAC Native American and African descendant populations is important for several reasons. First, studying human populations from different origins makes it possible to understand the diversity of the human genome better. Second, it also has an immediate application to these populations, such as empowering communities with the knowledge of their ancestral origins. Furthermore, because knowledge of the population genomic structure is an essential requirement for implementing genomic medicine and precision health practices, population genomics studies may ensure that these communities have access to genomic information for risk assessment, prevention, and the delivery of optimized treatment; thus, helping to reduce inequalities in the Western Hemisphere. Hoping to set the stage for future studies, we review different aspects related to genetic and genomic research in vulnerable populations from LAC countries.

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Inferring paternal history of rural African‐derived Brazilian populations from Y chromosomes

Cited by 6 publications

References 26 publications

The study of human Y chromosome variation through ancient DNA

The study of human Y chromosome variation through ancient DNA

Inbreeding estimates in human populations: Applying new approaches to an admixed Brazilian isolate

A review of ancestrality and admixture in Latin America and the caribbean focusing on native American and African descendant populations

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